Sunday, September 26, 2010

The Origin of Protein folds

Just trying to simplify the arguments of Axe in his review paper...

If we take E.coli as our model then the average length of a functional protein is around 300 amino acids.

If the protein is longer or if a number of different proteins are required to act in concert then the problem is made worse.

The number of possible sequences to be sampled to find functional proteins of this moderate size is vast...

There are two ways of reducing the sparse sampling problem.

(a) The number of possible sequences with a particular function is very large. Sequence space is rich in function.

(b) The functional sequences are in some way linked- once you have one function it is easy to jump to the next.

Axe argues that experimental results indicate that (a) is not big enough to solve the sparse search problem....

I will look at what he says about (b) next week!

29 Comments:

Anonymous Cedric Katesby said...

Axe argues that experimental results indicate...

If Axe wants to make experiments and demonstrate something then he should do so.
2004 was a long time ago.

A "Review Paper" is not worth much.
Less talky, talky and more worky, worky.

Nobody is taking the ball and running with it. Not Axe. Nor any of his friends.

If they are not excited enough to keep it going then that's a good indicator that they probably don't have anything to be excited about.

6:37 am  
Anonymous Mike Godfrey said...

And they say ID is a show stopper

9:32 am  
Blogger Psiloiordinary said...

Why are we looking at an evolved organism. Why not ask what the simplest protein might be?

Could he be hoping no one spots that little trick?

Did you Andrew?

Regards,

Psi

10:20 am  
Blogger Andrew Rowell said...

Psi,

No tricks intended.

I am simply trying to highlight the problem that Axe describes.

6:33 pm  
Blogger Andrew Rowell said...

Cedric,

I agree with you to a point...

However there is no point repeating experiments if you think you already have the answer.

6:34 pm  
Anonymous Cedric Katesby said...

30/September/2010
However there is no point repeating experiments if you think you already have the answer.

Nor is there any point in doing any follow-up research if you don't have anything interesting.

Everybody knows about Axe's work.
It's just that nobody is getting very worked up about it.
Nobody.
There's no conspiracy here.
Axe's natural allies are doing nothing except writing books and collecting money from speaking tours.

"The point which discredits ID is not that it has few peer-reviewed papers, but why there are so few. ID proponents appear to have no interest in conducting original research that would be appropriate for peer-reviewed journals, and other researchers see nothing in ID worth paying attention to. Despite empty claims that ID is a serious challenge to evolution, nobody takes ID seriously as a science, so nobody writes about it in the professional literature.

2.The papers and books cited by the Discovery Institute do not make a good case for peer-reviewed intelligent design for one or more reasons.

a.Many of the papers do not talk about design. Some do not even attempt to. For example:

•Axe (2000) finds that changing 20 percent of the external amino acids in a couple proteins causes them to lose their original function, even though individual amino acid changes did not. There was no investigation of change of function. Axe's paper is not even a challenge to Darwinian evolution, much less support for intelligent design. Axe himself has said that he has not attempted to make an argument for design in any of his publications (Forrest and Gross 2004, 42).
(...)

However, mainstream scientists recognize that science grows stronger through criticism, not through mere agreement, because criticism helps weed out the bad science. Most any evolutionary biologist can attest that supporting evolution is not enough to get a paper accepted; the paper has to describe sound science, too.
(...)
Publishing is not an end in itself. Scientific ideas mean nothing unless they can withstand criticism and be built upon. None of the "intelligent design" publications have led to any productive work."
Link

"Summary
To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

Acknowledgements:
Thanks to the efforts of the PT crew, and particularly Ian Musgrave, who helped me keep this on topic. Also, many thanks are due to Douglas Axe, who graciously helped me with early drafts of this essay. Please note that all of these ideas are mine, and I make no claim that any of these thoughts represent Axe’s views."
Link

Ultimately, not even creationists are excited by this. This is just another hobby-horse for them to ride.
Creationists don't care about protein folding.
Not really.
It's just a meme in a long series of sciency-sounding memes that always begin with "Science can't explain blah, blah, blah" or "Science got it wrong about blah, blah, blah..."

Then they go and shamelessly misrepresent some defenceless science experiment and present it to the rubes as a "funny" science story and it all ends up with "therefore magicmandunnit".

It's classic shtick.
Axe's experiment is just one more on the pile.Lee Strobel does it all the time.

5:58 pm  
Anonymous Anonymous said...

Cedric Katesby
I’m afraid that creationists do not (or do!) care about protein folding is not a scientific or philosophical argument against need for intelligence in protein folding. You still need to show how blind forces can assemble the machinery that makes proteins.

It’s my ID position that successful folding requires co-ordination between Nuclei & Ribosomal codes. No such co-ordination can happen without consciousness. This is based on what we KNOW. Yet saying blind forces can do this is based on what is NOT KNOWN.

If you show me how matter alone can co-ordinate 2 separate codes I will believe in evolution.

9:32 pm  
Anonymous Cedric Katesby said...

9/October/2010

...against need for intelligence in protein folding.

Nobody is arguing that there needs to be intelligence in protein folding.
Certainly not Axe.
He doesn't mention it at all in any of his research.

If you want to make such an argument then go right ahead.
Please do.
Could be interesting.
Present your evidence.

Yet I don't see how you can do so and yet avoid falling into a simple argument from ignorance.

You still need to show how blind forces...

"Blind forces"?
Huh?

You are saying that whatever you are arguing for must be true based upon the weakness of the other guy's position.
The other guy needs to demonstrate something to you, otherwise your postion must be true...by default.
Nope.
Science doesn't work that way.
That's just a cop-out.

If you show me how matter alone can co-ordinate 2 separate codes I will believe in evolution.

No.
Forget all the evolution stuff.
Ignore it all.

Here's how it works:

Go ahead and ditch evolution.
Go ahead.
Do it.
Take it out of the running completely.
Flush it down the toilet.
All of it.

That does not add any credibility to any other position...not even yours.

Doesn't work.
You still are still left with a whole lot of nothing even without the big bad old Theory of Evolution to contend with.

If you have a scientific theory that does a better job of explaining proteins then it must have actual positive evidence to support it.

Dismissing some other theory does not help out your position at all.
(Even if your criticisms are perfectly valid and well-accepted by everybody, including me.)
Still doesn't help.
Not even a little bit.

False dichotomy.

It’s my ID position...

Yay.
Somebody at last has a position on ID.
Great.
Finally.

You have no idea how many supporters of ID on this ID-friendly web-site seem to be utterly clueless about what ID really means.

I'm sure you are not among their number.

What's ID?
I say that it's a meaningless buzzword that has no scientfic definition and that you can't take it into the lab and do something useful with it.

What do you say?
What's ID?

1:06 am  
Anonymous Anonymous said...

Cedric Katesby
You are saying you don’t know how protein folding could happen without intelligence but insist we believe it happened that way. You are also asking us not think it happened with intelligence even if we know that it would require intelligence. Have I understood you correctly?

3:45 pm  
Anonymous Cedric Katesby said...

11/October/2010

You are saying you don’t know how protein folding could happen without intelligence but insist we believe it happened that way.

Not at all.
I'm not insisting you believe anything.

I'm just pointing out that criticisms of a scientific theory (whether real or imagined, valid or invalid) do not magically add up to support for some other theory.

You are also asking us not think it happened with intelligence...

By all means think what you like.

Yet if you want to propose a new theory that better explains things...then you must produce positive evidence for such a theory.
No good poo-pooing any other theory.
Science does not work that way.
It can't.

...if we know that it would require intelligence.

If you really "know" that, as opposed to just believe that, then go do some work.

Demonstrate that it is so.
Get thee hence to a lab.
Do some work.
Axe has not done so.

He does not mention anything about the need for intelligence in any of his research.
Never.
Nor have any of his friends.
It's been years now.
There's been sweet stuff all.

Now let's talk about ID.
After all, this blog is devoted to discussion of ID.
And you are a supporter of ID.
Happy, happy, happy me.

:)


It’s my ID position...

Yay.
Somebody at last has a position on ID.
Great.
Finally.

You have no idea how many supporters of ID on this ID-friendly web-site seem to be utterly clueless about what ID really means.

I'm sure you are not among their number.

What's ID?
I say that it's a meaningless buzzword that has no scientfic definition and that you can't take it into the lab and do something useful with it.

What do you say?
What's ID?
Let's hear it.
Don't skimp on the details.

5:33 pm  
Anonymous Anonymous said...

Cedric Katesby
You are right that criticism of a scientific theory doesn’t make an alternative true by default. But would you also agree it makes the one rightly criticised false?

You ask for positive evidence for the necessity of Intelligence in production of co-ordinated operations such as between nucleic & ribosomal codes. What kind of evidence would persuade you?

11:49 pm  
Anonymous Cedric Katesby said...

(Re-post from a couple of days ago)

13/10/2010

But would you also agree it makes the one rightly criticised false?

No.
That's not the way scientific theories work.
Legitimate criticisms can be leveled at many different scientific theories.
That does not stop them from being useful.

The path of science is littered with falsified scientific theories.
A scientific theory is not a popularity contest.
It does not exist because scientists prefer it or like it or find it comforting.
It's not a testament of faith that must be clung to at all costs.

Scientific theories remain mainstream only for as long as they are useful.
If a scientific theory does not help direct research by making predictions or providing a systematic framework to explain data then it gets ditched in favour of something better.


ID is not "something better".

ID has nothing to offer the working scientist.
Nothing. Zippo. Nada.
A big, fat, hairy, zero.
A total waste of time.

It's physically impossible to do any work with ID.
It's quite literally a research dead end.
Just ask Axe.

Yet, on the other hard, you can do stuff with the Theory of Evolution.
You can discover new things.
You can perform experiments and plan new research.
The Theory of Evolution is valuable.
It's fruitful.
It helps medical scientists and biologists do their job properly.

You ask for positive evidence for the necessity of Intelligence in production of co-ordinated operations such as between nucleic & ribosomal codes. What kind of evidence would persuade you?

I'd need to understand what you mean by "intelligence" for a start.

ID is meaningless.
No, really.
It's just a slogan.

Search as much as you like but you won't find a viable, no-nonsense scientific definition of Intelligent Design anywhere.

Nobody has ever bothered to even try.

A determined amount of digging into the meaning of ID reveals nothing more than fuzzy analogies and vague hand-waving.

You can't march into a lab and get some serious work done with the pablum than the Discovery Institute dribbles out.

There's nothing concrete.
It's a scam.

The people that told you that ID is a super-duper sciency thing are either themselves decieved or are decievers themselves.

You've been lied to.

2:10 pm  
Anonymous Anonymous said...

Cedric katesby
I don’t mean this is a bad way but some of your responses sound more like complaints about the very existence of ID without any reference to its merits or lack thereof. So I have a suggestion: How about you give a brief answer to this. What’s the ONE logical problem you have with ID?

8:04 pm  
Anonymous Cedric Katesby said...

14/October/2010

I don’t mean this is a bad way but some of your responses sound more like complaints about the very existence of ID...

ID doesn't exist.
It's a meaningless, fuzzy, hand-wavey phrase.
Nothing more.

...without any reference to its merits or lack thereof.

An empty, meaningless phrase has few merits.
Hand-waving fuzziness remains hand-wavey fuzziness.

What’s the ONE logical problem you have with ID?

ID is meaningless.
You can't do anything with it.

That's the reason why nobody is doing anything with it.


No experiments.
No work.
Not even a usable scientific definition.
Over twenty years of stuff all.

I can't make it any clearer than that.

It's a fraud.

12:52 am  
Anonymous Anonymous said...

You said ID doesn’t exist & it’s fraud. Both these statements can’t be true because for something to be fraudulent, 1st of all it must exist. So which is it?

How do you know If ID is fraudulent? I presume you base this charge on scientific tests that have shown it’s fraudulent. But this creates you a dilemma. If ID is unscientific, how did you scientifically test this? This should also deal with your charge that there are no experiments for ID. We have at least one experiment i.e. the test which showed ID to be unscientific. How do will you get out of this dilemma?

Finally, it is perfectly logical for something to be completely non-existent, unscientific or fraudulent. So neither of these (non-existence, unscientific or fraudulent) are logical refutations of ID. That leaves my question unanswered: What is your logical problem with ID?

10:03 pm  
Anonymous Cedric Katesby said...

15/October/2010

You said ID doesn’t exist & it’s fraud. Both these statements can’t be true because for something to be fraudulent, 1st of all it must exist.

Wow.

"You said the Cottinglay fairies doesn’t exist & it’s fraud. Both these statements can’t be true because for something to be fraudulent, 1st of all it must exist."


If ID is unscientific, how did you scientifically test this? This should also deal with your charge that there are no experiments for ID.

Double wow.

"If alien space-magic is unscientific, how did you scientifically test this? This should also deal with your charge that there are no experiments for alien space-magic."


Finally, it is perfectly logical for something to be completely non-existent, unscientific or fraudulent.

Why yes.
I suppose it is.
Something can be completely non-existent and yet be perfectly logical.

Something can be completly unscientific and yet be perfectly logical.

Something can be completely fraudulent and yet be perfectly logical.


That leaves my question unanswered: What is your logical problem with ID?

Behold the awesome power of ID.
Modern biology, tremble in fear.

All science, all the time.
:)

11:52 pm  
Anonymous Anonymous said...

Cedric Katesby
The question still remains: What is your logical objection to ID?

9:25 pm  
Anonymous Cedric Katesby said...

16/October/2010

The question still remains: What is your logical objection to ID?

Oh nothing.
Nothing at all.
I have no "logical objections" to ID whatsoever.
Really.

It's just that...well...

Umm...

What do you mean when you say "ID"?
What is it?

Do you have a scientific definition for it or is it just a meaningless, vague buzzword?

11:41 pm  
Anonymous Anonymous said...

If you have no logical problem with ID, what kind(s) of problem(s) do you have with it?

There is no scientific definition of science or evolution & ID is no different. All definitions are philosophical. If you disagree, please give a SCIENTIFIC (from observation or experiments) definition of science.

We therefore still need an answer as to what problems you have with ID. We've established they are not logical or scientific. Please tell us what they are.

11:00 pm  
Anonymous Cedric Katesby said...

18/October/2010

There is no scientific definition of science or evolution & ID is no different.

Wow.
No scientific definitions?
Not even of science itself?
Wow.

All definitions are philosophical.

All of them?
Well, that's very surprising.

;)

So just to be clear (and to stay firmly on topic)...you are saying that there is no scientific definition of ID?
Right?

1:03 am  
Anonymous Anonymous said...

"you are saying that there is no scientific definition of ID?"

......There is no scientific definition of science. It doesn't matter whether you apply this to physics, ID or evolution - the definition is still philosophical.

So again, what is your logical problem with ID?

10:37 pm  
Anonymous Anonymous said...

Cedric Katesby
“You are saying that there is no scientific definition of ID?”

.......Correct. Scientific knowledge is gained by testing either with experiments or observation. A definition is neither an experiment or observation. It’s a philosophical statement. This applies to all definitions, including of science. (Philosophy precedes science).

Having cleared the above, can you please tell us what your logical objection to ID is?

10:08 pm  
Anonymous Cedric Katesby said...

21/October/2010

Scientific blah, blah, blah... A definition is neither blah, blah, blah...Philosophy blah, blah..

“You are saying that there is no scientific definition of ID?”

.......Correct.

Finally. We get to the truth.
Took you long enough.

Having cleared the above, can you please tell us what your logical objection to ID is?

Huh?
We've already covered this.

I have no "logical objections" to ID whatsoever.
Really.

;)

"Logical objections" don't enter into it.

You don't have a scientific definition for ID.
That says it all.
Stick a fork in it.
It's done.

ID is just vague, fluffy nonsense to fool the gullible into believing that something sciency is going on.
Dig patiently past the purile word-games and hapless hand-waving and you end up with a big, fat fraud.

ID is a joke.
Not even their own supporters take it seriously.

6:33 pm  
Anonymous Anonymous said...

On the one hand you say logical objections don’t apply & on the other hand, you say you have no logical objections to ID. But both statements can’t be true at the same time, aren’t you contradicting yourself?

11:51 pm  
Anonymous Cedric Katesby said...

21/October/2010

And the stupid word-games continue...

On the one hand you say logical objections don’t apply & on the other hand, you say you have no logical objections to ID.

No, you are suffering from an basic reading comprehension fail.
(Self-induced, I suspect.)

...you say you have no logical objections to ID.

No, this is what I wrote...

I have no "logical objections" to ID whatsoever.
Really.

;)


Spot the difference.
Think about it.
Try a little.

...you say logical objections don’t apply &...

They don't.
You are the one harping on about logical objections.
Not me.
You are bringing up that phrase as a purile word-game because you don't have anything.

...it is perfectly logical for something to be completely non-existent, unscientific or fraudulent.

Why yes.
I suppose it is.
Something can be completely non-existent and yet be perfectly logical.

Something can be completly unscientific and yet be perfectly logical.

Something can be completely fraudulent and yet be perfectly logical.

"Logical objections" don't enter into it.

This is about ID.
You are a self-confessed supporter of ID.

What's ID?
I say that it's a meaningless buzzword that has no scientfic definition and that you can't take it into the lab and do something useful with it.

What do you mean when you say "ID"?
What is it?

Do you have a scientific definition for it or is it just a meaningless, vague buzzword?


What do you say?
What's ID?
Let's hear it.
Don't skimp on the details.

(Anonymous babbles on uselessly for a few comments. He has nothing to say. He has no idea what he is talking about. His words are empty shell games.)

ID is just vague, fluffy nonsense to fool the gullible into believing that something sciency is going on.
Dig patiently past the purile word-games and hapless hand-waving and you end up with a big, fat fraud.

ID is a joke.
Not even their own supporters take it seriously.

9:44 am  
Blogger Psiloiordinary said...

Here you go;

http://www.youtube.com/user/cdk007#p/u/13/qLnr_3J1IT8

4:21 pm  
Blogger Andrew Rowell said...

Thanks for that Psi,

I will look into the novel protein creation paper.

4:46 pm  
Blogger Andrew Rowell said...

Psi,

This is the paper that is mentioned in CDK007 origin of genes video:

Experimental Rugged Fitness Landscape in Protein Sequence Space

I am having a look at it.

9:05 am  
Anonymous Cedric Katesby said...

13/Novemeber/2010

This is the paper that is mentioned in CDK007 origin of genes video...

CDK oo7 is..the devil.
He may come across as reasonable and sane and with a higher appreciation of classical music but he is a monster.
This is a person that eats babies.
This is a person that flings poo from trees.
This is a person that will send you to hell with his lies and deciet!

Or not.

Yet why take the risk?
Listen only to the Discovery Institute.
They have your best interests at heart.
They have never lied to you or said anything dodgy.
Trust them.

11:20 am  

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